libAMOS: AMOS::Read_t Class Reference

AMOS::Read_t::Read_t ( ) [inline]

Constructs an empty Read_t object.

Sets all members to NULL

Definition at line 76 of file Read_AMOS.hh.

References AMOS::NULL_ID, and NULL_READ.

AMOS::Read_t::Read_t ( const Read_t & source ) [inline]

Copy constructor.

Definition at line 87 of file Read_AMOS.hh.

AMOS::Read_t::~Read_t ( ) [inline]

Destroys a Read_t object.

Definition at line 96 of file Read_AMOS.hh.

void Read_t::clear ( ) [virtual]

Clears all object data, reinitializes the object.

All data will be cleared, but object compression status will remain unchanged. Use the compress/uncompress members to change this info.

Reimplemented from AMOS::Sequence_t.

Definition at line 22 of file Read_AMOS.cc.

References AMOS::Sequence_t::clear(), AMOS::NULL_ID, and NULL_READ.

Referenced by readMessage(), setClearRange(), and writeMessage().

void Sequence_t::compress ( ) [inherited]

Compress the internal representation of this sequence.

After compression, this object will continue to compress incoming data until the uncompress method is called. Compression packs both a base and a quality score into a single byte, effectively halving the memory requirements for each object.

The sequence should only contain A,C,G,T and Ns and quality scores in the range [MIN_QUALITY,MAX_QUALITY], if either of these conditions are not met the information will be lost when the data is compressed (see postconditions below).

Postcondition:

All invalid quality scores will be cast to MIN_QUALITY

All N's will be assigned a MIN_QUALITY quality score

All MIN_QUALITY scores will be assigned a N seqchar

Returns:: void

Definition at line 37 of file Sequence_AMOS.cc.

References AMOS::Sequence_t::COMPRESS_BIT, AMOS::IBankable_t::flags_m, AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::Sequence_t::qual_m, and AMOS::Sequence_t::seq_m.

Referenced by AMOS::Sequence_t::clear(), and AMOS::Sequence_t::setBase().

static uint8_t AMOS::Sequence_t::compress	(	char	seqchar,
		char	qualchar
	)			`[inline, static, protected, inherited]`

Compresses a sequence char and quality char into a single byte.

Note:: Must work with uncompress(uint8_t) method

Parameters:

	seqchar	The sequence base character (case insensitive)
	qualchar	The quality score character

Returns:: The compressed byte

Definition at line 64 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::ADENINE_BITS, AMOS::Char2Qual(), AMOS::Sequence_t::CYTOSINE_BITS, AMOS::Sequence_t::GUANINE_BITS, AMOS::Sequence_t::SEQ_BITS, and AMOS::Sequence_t::THYMINE_BITS.

std::pair<char, char> AMOS::Sequence_t::getBase ( Pos_t index ) const [inline, inherited]

Get a single base and its quality score.

Retrieves and uncompresses the sequence base for the requested index.

Parameters:

index

The index of the requested base

Precondition:: index >= 0 && index < length

Exceptions:

ArgumentException_t

Returns:: The requested (uppercase) base character and its quality score

Definition at line 205 of file Sequence_AMOS.hh.

References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::Sequence_t::qual_m, AMOS::Sequence_t::seq_m, and AMOS::Sequence_t::uncompress().

Referenced by AMOS::Sequence_t::getGCContent(), AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), AMOS::Contig_t::getUngappedLength(), AMOS::Contig_t::getUngappedQualString(), AMOS::Contig_t::getUngappedSeqString(), and AMOS::Sequence_t::writeMessage().

std::vector<int16_t>& AMOS::Read_t::getBasePositions ( ) [inline]

Get the base call positions.

If the vector is empty, then no base call positions are provided. Otherwise, the vector should have a size equal to the sequence length representing the base call positions as specified by the base-caller.

Returns:: The vector of base call positions

Definition at line 130 of file Read_AMOS.hh.

const std::vector<int16_t>& AMOS::Read_t::getBasePositions ( ) const [inline]

Get the base call positions.

If the vector is empty, then no base call positions are provided. Otherwise, the vector should have a size equal to the sequence length representing the base call positions as specified by the base-caller.

Returns:: The vector of base call positions

Definition at line 115 of file Read_AMOS.hh.

Range_t AMOS::Read_t::getClearRange ( ) [inline]

Get the generic clear range.

Returns:: The generic clear range

Definition at line 141 of file Read_AMOS.hh.

Referenced by AMOS::operator<<().

const std::string& AMOS::Universal_t::getComment ( ) const [inline, inherited]

Get the comment string.

Returns:: The comment string

Definition at line 116 of file Universal_AMOS.hh.

Referenced by AMOS::operator<<().

const std::string& AMOS::IBankable_t::getEID ( ) const [inline, inherited]

Get the external ID.

Returns:: The external ID

Definition at line 174 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m.

Referenced by AMOS::TiledRead_t::TiledRead_t().

ID_t AMOS::Read_t::getFragment ( ) const [inline]

Get the parent fragment IID.

Returns:: The parent fragment IID

Definition at line 152 of file Read_AMOS.hh.

Pos_t AMOS::Read_t::getFragmentPosition ( ) [inline]

Get the approximate position on the parent fragment.

Get this read's 1-based position on the parent fragment, positive if counting from left and oriented forward, negative if counting from right and reverse oriented, 0 if unknown.

Returns:: The position of this read on the parent fragment

Definition at line 167 of file Read_AMOS.hh.

virtual double AMOS::Sequence_t::getGCContent ( ) const [inline, virtual, inherited]

Get the gc content of the sequence.

Returns:: The gc content of the full range of the sequence

Reimplemented in AMOS::Contig_t.

Definition at line 260 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::length_m.

virtual double AMOS::Sequence_t::getGCContent ( const Range_t & rng ) const [inline, virtual, inherited]

Get the gc content of the sequence.

Returns:: The gc content for the specified range of the sequence

Reimplemented in AMOS::Contig_t.

Definition at line 226 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::getBase(), AMOS::Range_t::getHi(), and AMOS::Range_t::getLo().

ID_t AMOS::IBankable_t::getIID ( ) const [inline, inherited]

Get the internal ID.

Returns:: The internal ID

Definition at line 185 of file Bank_AMOS.hh.

References AMOS::IBankable_t::iid_m.

Referenced by AMOS::Index_t::buildContigFeature(), AMOS::Index_t::buildContigScaffold(), AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildScaffoldFeature(), and AMOS::operator<<().

Size_t AMOS::Sequence_t::getLength ( ) const [inline, inherited]

Get the length of the sequence.

Returns:: The length of the sequence

Definition at line 272 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::length_m.

Referenced by AMOS::Contig_t::getAvgRho(), AMOS::Contig_t::getSpan(), AMOS::Contig_t::getUngappedQualString(), AMOS::Contig_t::getUngappedSeqString(), and writeMessage().

virtual NCode_t AMOS::Read_t::getNCode ( ) const [inline, virtual]

Get the AMOS NCode type identifier.

Returns:: The AMOS NCode type identifier

Reimplemented from AMOS::Sequence_t.

Definition at line 174 of file Read_AMOS.hh.

References NCODE.

Range_t AMOS::Read_t::getQualityClearRange ( ) [inline]

Get the quality score clear range.

Returns:: The quality score clear range

Definition at line 185 of file Read_AMOS.hh.

string Sequence_t::getQualString ( Range_t range ) const [inherited]

Get a quality score substring.

Returns a subrange of quality scores [begin, end) or (end, begin]. The reversed range will pull the reverse string of quality scores.

Parameters:

range

The range of quality scores to get

Precondition:: range lo >= 0 && hi <= length

Exceptions:

ArgumentException_t

Returns:: A subrange quality scores

Definition at line 59 of file Sequence_AMOS.cc.

References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::getBase(), AMOS::Sequence_t::length_m, AMOS::NULL_CHAR, and AMOS::Reverse().

std::string AMOS::Sequence_t::getQualString ( ) const [inline, inherited]

Get the quality score string.

Returns:: The full string of quality scores

Definition at line 290 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::length_m.

Referenced by AMOS::ContigIterator_t::ContigIterator_t(), AMOS::Contig_t::insertGapColumn(), AMOS::operator<<(), and AMOS::Contig_t::reverseComplement().

string Sequence_t::getSeqString ( Range_t range ) const [inherited]

Get a sequence base substring.

Returns a subrange of sequence bases [begin, end) or (end, being]. The reversed range will pull the reverse complement string of sequences bases.

Parameters:

range

The range of sequence bases to get

Precondition:: range lo >= 0 && hi <= length

Exceptions:

ArgumentException_t

Returns:: A subrange of sequence bases

Definition at line 83 of file Sequence_AMOS.cc.

References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::getBase(), AMOS::Sequence_t::length_m, AMOS::NULL_CHAR, and AMOS::ReverseComplement().

std::string AMOS::Sequence_t::getSeqString ( ) const [inline, inherited]

Get the sequence base string.

Returns:: The full string of sequence bases

Definition at line 315 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::length_m.

Referenced by AMOS::ContigIterator_t::ContigIterator_t(), AMOS::Contig_t::insertGapColumn(), AMOS::operator<<(), and AMOS::Contig_t::reverseComplement().

const Status_t AMOS::Universal_t::getStatus ( ) const [inline, inherited]

Get the status value.

Returns:: The status value

Definition at line 127 of file Universal_AMOS.hh.

ReadType_t AMOS::Read_t::getType ( ) const [inline]

Get the type of read.

Returns:: The type of read

Definition at line 196 of file Read_AMOS.hh.

Range_t AMOS::Read_t::getVectorClearRange ( ) [inline]

Get the vector sequence clear range.

Returns:: The vector sequence clear range

Definition at line 207 of file Read_AMOS.hh.

bool AMOS::Sequence_t::isCompressed ( ) const [inline, inherited]

Checks if the sequence data is compressed.

Returns true if the Sequence is currently operating in compressed mode, or false if under normal operation.

Returns:: True if compressed, false if not

Definition at line 343 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::COMPRESS_BIT, and AMOS::IBankable_t::flags_m.

Referenced by AMOS::Sequence_t::compress(), AMOS::Sequence_t::getBase(), AMOS::Sequence_t::operator=(), AMOS::Sequence_t::setBase(), AMOS::Sequence_t::setSequence(), and AMOS::Sequence_t::uncompress().

bool AMOS::IBankable_t::isFlagA ( ) const [inline, inherited]

Check the value of flag A.

Returns:: The value of flag A

Definition at line 228 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isFlagB ( ) const [inline, inherited]

Check the value of flag B.

Returns:: The value of flag B

Definition at line 239 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isModified ( ) const [inline, inherited]

Check if the object has been modified.

Returns:: true if modified, otherwise false

Definition at line 217 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

bool AMOS::IBankable_t::isRemoved ( ) const [inline, inherited]

Check if the object is waiting to be removed from the bank.

Note:: Useful for debugging only

Returns:: true if removed, otherwise false

Definition at line 206 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

void Read_t::readMessage ( const Message_t & msg ) [virtual]

Reads in data from a Message object.

Reads the data contained in a Message object and stores it in the Messagable object. Will not complain if incoming message is of the wrong type, will only try and suck out the fields it recognizes. All previous data in the Messagable object will be cleared or overwritten.

Parameters:

msg

The Message to read from

Precondition:: The expected fields are formatted properly

Exceptions:

ArgumentException_t

Returns:: void

Reimplemented from AMOS::Sequence_t.

Definition at line 36 of file Read_AMOS.cc.

References AMOS_THROW_ARGUMENT, clear(), AMOS::F_BASEPOSITION, AMOS::F_CLEAR, AMOS::F_FRAGMENT, AMOS::F_POSITION, AMOS::F_QUALITYCLEAR, AMOS::F_TYPE, AMOS::F_VECTORCLEAR, AMOS::Sequence_t::readMessage(), and setType().

virtual void AMOS::Read_t::readRecord	(	std::istream &	fix,
		std::istream &	var
	)			`[protected, virtual]`

Read selected class members from a biserial record.

Reads the fixed and variable length streams from a biserial record and initializes the class members to the values stored within. Used in translating a biserial IBankable object, and needed to retrieve objects from a bank.

Note:: This method must be able to interpret the biserial record produced by its related function writeRecord.

Parameters:

	fix	The fixed length stream (stores all fixed length members)
	var	The variable length stream (stores all var length members)

Precondition:: The get pointer of fix is at the beginning of the record
The get pointer of var is at the beginning of the record

Returns:: void

Reimplemented from AMOS::Sequence_t.

virtual void AMOS::Read_t::readRecordFix ( std::istream & fix ) [protected, virtual]

Read selected class members from a fixed store only.

Reads the fixed stream and initializes the class members to the values stored within. Used to fetch the fixed portion of a biserial IBankable object, and needed to retrieve objects from a bank.

Note:: This method must be able to interpret the biserial record produced by its related function writeRecord.

Parameters:

fix

The fixed length stream (stores all fixed length members)

Precondition:: The get pointer of fix is at the beginning of the record

Returns:: void

Reimplemented from AMOS::Sequence_t.

void AMOS::Sequence_t::setBase	(	char	seqchar,
		char	qualchar,
		Pos_t	index
	)			`[inline, inherited]`

Set a sequence base and its quality score.

Any characters may be used for seq and qualchar unless dealing with a compressed sequence. If compressed, the sequence should only contain A,C,G,T and Ns and quality scores in the range [MIN_QUALITY,MAX_QUALITY], if either of these conditions are not met the information will be lost when the data is compressed (see postconditions below).

Parameters:

	seqchar	The sequence base character
	qualchar	The quality score character
	index	The index to assign these values

Precondition:: index >= 0 && index < length

Postcondition:

If compressed:

All invalid quality scores will be cast to MIN_QUALITY
All N's will be assigned a MIN_QUALITY quality score
All MIN_QUALITY scores will be assigned a N seqchar

Exceptions:

ArgumentException_t

Returns:: void

Definition at line 373 of file Sequence_AMOS.hh.

References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::compress(), AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::Sequence_t::qual_m, and AMOS::Sequence_t::seq_m.

Referenced by AMOS::Sequence_t::setSequence().

void AMOS::Read_t::setBasePositions ( const std::vector< int16_t > & bcp ) [inline]

Set the base call positions.

Parameters:

bcp

The new vector of base call positions

Returns:: void

Definition at line 223 of file Read_AMOS.hh.

void AMOS::Read_t::setClearRange ( Range_t clear ) [inline]

Set the generic clear range.

Parameters:

clear

The new generic clear range

Returns:: void

Definition at line 235 of file Read_AMOS.hh.

References clear().

void AMOS::Universal_t::setComment ( const std::string & comment ) [inline, inherited]

Set the comment string.

Parameters:

comment

The new comment string

Returns:: void

Definition at line 150 of file Universal_AMOS.hh.

void AMOS::IBankable_t::setEID ( const std::string & eid ) [inline, inherited]

Set the external ID.

Will only use the characters up to but not including the first newline.

Returns:: void

Definition at line 252 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m, and AMOS::NL_CHAR.

void AMOS::IBankable_t::setFlagA ( bool flag ) [inline, inherited]

Set flag A.

Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag B.

Parameters:

flag

The new flag A value

Returns:: void

Definition at line 272 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::IBankable_t::setFlagB ( bool flag ) [inline, inherited]

Set flag B.

Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag A.

Parameters:

flag

The new flag B value

Returns:: void

Definition at line 288 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::Read_t::setFragment ( ID_t frag ) [inline]

Set the parent fragment IID.

Parameters:

frag

The new parent fragment IID

Returns:: void

Definition at line 247 of file Read_AMOS.hh.

void AMOS::Read_t::setFragmentPosition ( Pos_t pos ) [inline]

Set the approximate position on the parent fragment.

Set this read's 1-based position on the parent fragment, positive if counting from left and oriented forward, negative if counting from right and reverse oriented, 0 if unknown.

Parameters:

pos

The approximate position of this read on the parent fragment

Returns:: void

Definition at line 263 of file Read_AMOS.hh.

void AMOS::IBankable_t::setIID ( ID_t iid ) [inline, inherited]

Set the internal ID.

Parameters:

iid

The new internal ID

Returns:: void

Definition at line 300 of file Bank_AMOS.hh.

References AMOS::IBankable_t::iid_m.

void AMOS::Read_t::setQualityClearRange ( Range_t qclear ) [inline]

Set the quality score clear range.

Parameters:

qclear

The new quality score clear range

Returns:: void

Definition at line 275 of file Read_AMOS.hh.

void AMOS::Sequence_t::setSequence	(	const std::string &	seq,
		const std::string &	qual
	)			`[inherited]`

Set the entire sequence.

Combines and compresses the sequence and quality data contained in the two STL strings. If current Sequence object is compressed, please refer to the postconditions for the setBase(char,char,Pos_t) operation. All newline characters will be discarded. but the newlines must be in the same location in both the sequence and quality files.

Parameters:

	seq	The sequence base string
	qual	The quality score string

Precondition:: seq . size( ) == qual . size( )

Exceptions:

ArgumentException_t

Returns:: void

Reimplemented in AMOS::Contig_t.

void Sequence_t::setSequence	(	const char *	seq,
		const char *	qual
	)			`[inherited]`

Set the entire sequence.

Combines and compresses the sequence and quality data contained in the two C strings. If current Sequence object is compressed, please refer to the postconditions for the setBase(char,char,Pos_t) operation. All newline characters will be discarded, but the newlines must be in the same location in both the sequence and quality files.

Parameters:

	seq	The sequence base string
	qual	The quality score string

Precondition:: strlen(seq) == strlen(qual)

Exceptions:

ArgumentException_t

Returns:: void

Reimplemented in AMOS::Contig_t.

Definition at line 163 of file Sequence_AMOS.cc.

References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::NL_CHAR, AMOS::Sequence_t::qual_m, AMOS::SafeRealloc(), and AMOS::Sequence_t::setBase().

Referenced by AMOS::Sequence_t::readMessage(), and AMOS::Contig_t::setSequence().

void AMOS::Universal_t::setStatus ( Status_t status ) [inline, inherited]

Set the status value.

Parameters:

status

The new status value

Returns:: void

Definition at line 162 of file Universal_AMOS.hh.

Referenced by AMOS::Universal_t::readMessage().

void Read_t::setType ( ReadType_t type )

Set the type of read.

Parameters:

type

The new type of read

Precondition:: type is one of [XECBW]

Exceptions:

ArgumentException_t

Returns:: void

Definition at line 170 of file Read_AMOS.cc.

References AMOS_THROW_ARGUMENT, BAC, CONTIG, END, NULL_READ, OTHER, TRANSPOSON, and WALK.

Referenced by readMessage().

void AMOS::Read_t::setVectorClearRange ( Range_t vclear ) [inline]

Set the vector sequence clear range.

Parameters:

vclear

The new vector sequence clear range

Returns:: void

Definition at line 298 of file Read_AMOS.hh.

void Sequence_t::uncompress ( ) [inherited]

Uncompress the internal representation of this sequence.

After uncompression, this object will not compress incoming data until the compress method is called once again. The uncompressed version uses two bytes to store a base and quality score, thus doubling the memory requirements over a compressed version.

Returns:: void

Definition at line 231 of file Sequence_AMOS.cc.

References AMOS::Sequence_t::COMPRESS_BIT, AMOS::IBankable_t::flags_m, AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, and AMOS::SafeRealloc().

Referenced by AMOS::Sequence_t::getBase().

static std::pair<char, char> AMOS::Sequence_t::uncompress ( uint8_t byte ) [inline, static, protected, inherited]

Uncompresses a byte into a sequence and quality char.

Note:: Must work with compress(char,char)

Parameters:

byte

The compressed sequence and quality byte

Returns:: The sequence and quality char respectively

Definition at line 93 of file Sequence_AMOS.hh.

References AMOS::Sequence_t::ADENINE_BITS, AMOS::Sequence_t::CYTOSINE_BITS, AMOS::Sequence_t::GUANINE_BITS, AMOS::Qual2Char(), AMOS::Sequence_t::QUAL_BITS, AMOS::Sequence_t::SEQ_BITS, and AMOS::Sequence_t::THYMINE_BITS.

void Read_t::writeMessage ( Message_t & msg ) const [virtual]

Writes data to a Message object.

Writes the data contained in a Messagable object to a Message object. All previous data in the Message will be cleared or overwritten.

Parameters:

msg

The Message to write to

Returns:: void

Reimplemented from AMOS::Sequence_t.

Definition at line 190 of file Read_AMOS.cc.

References clear(), AMOS::F_BASEPOSITION, AMOS::F_CLEAR, AMOS::F_FRAGMENT, AMOS::F_POSITION, AMOS::F_QUALITYCLEAR, AMOS::F_TYPE, AMOS::F_VECTORCLEAR, AMOS::Sequence_t::getLength(), NCODE, AMOS::NULL_ID, NULL_READ, AMOS::NULL_STRING, and AMOS::Sequence_t::writeMessage().

virtual void AMOS::Read_t::writeRecord	(	std::ostream &	fix,
		std::ostream &	var
	)			const `[protected, virtual]`

Write selected class members to a biserial record.

Writes the fixed and variable length streams to a biserial record. Used in generating a biserial IBankable object, and needed to commit objects to a bank. Should not write the flags, EID, or IID of the object because the bank will handle the storage of these fields on its own.

Note:: This method must be able to produce a biserial record that can be read by its related funtion readRecord.

Parameters:

	fix	The fixed length stream (stores all fixed length members)
	var	The variable length stream (stores all var length members)

Returns:: void

Reimplemented from AMOS::Sequence_t.

const uint8_t AMOS::Sequence_t::ADENINE_BITS = 0x0 [static, protected, inherited]

'A' bit

Definition at line 47 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

const ReadType_t AMOS::Read_t::BAC = 'B' [static]

Definition at line 66 of file Read_AMOS.hh.

Referenced by setType().

const uint8_t AMOS::Sequence_t::COMPRESS_BIT = 0x1 [static, protected, inherited]

compressed sequence flag

Definition at line 46 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::clear(), AMOS::Sequence_t::compress(), AMOS::Sequence_t::isCompressed(), and AMOS::Sequence_t::uncompress().

const ReadType_t AMOS::Read_t::CONTIG = 'C' [static]

Definition at line 65 of file Read_AMOS.hh.

Referenced by setType().

const uint8_t AMOS::Sequence_t::CYTOSINE_BITS = 0x40 [static, protected, inherited]

'C' bit

Definition at line 48 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

std::string AMOS::IBankable_t::eid_m [protected, inherited]

external ID (anything you want sans newlines)

Definition at line 66 of file Bank_AMOS.hh.

Referenced by AMOS::Bank_t::append(), AMOS::IBankable_t::clear(), AMOS::IBankable_t::getEID(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Universal_t::readMessage(), AMOS::BankStream_t::replace(), AMOS::Bank_t::replace(), AMOS::BankStream_t::replaceByBID(), AMOS::IBankable_t::setEID(), and AMOS::Universal_t::writeMessage().

const ReadType_t AMOS::Read_t::END = 'E' [static]

Definition at line 64 of file Read_AMOS.hh.

Referenced by setType().

BankFlags_t AMOS::IBankable_t::flags_m [protected, inherited]

const uint8_t AMOS::Sequence_t::GUANINE_BITS = 0x80 [static, protected, inherited]

'G' bit

Definition at line 49 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

ID_t AMOS::IBankable_t::iid_m [protected, inherited]

internal ID (integer AMOS identifier)

Definition at line 64 of file Bank_AMOS.hh.

Referenced by AMOS::Bank_t::append(), AMOS::IBankable_t::clear(), AMOS::IBankable_t::getIID(), AMOS::IBankable_t::IBankable_t(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Universal_t::readMessage(), AMOS::BankStream_t::replace(), AMOS::Bank_t::replace(), AMOS::BankStream_t::replaceByBID(), AMOS::IBankable_t::setIID(), and AMOS::Universal_t::writeMessage().

Size_t AMOS::Sequence_t::length_m [protected, inherited]

length of the sequence and quality data

Definition at line 43 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::clear(), AMOS::Sequence_t::compress(), AMOS::Sequence_t::getBase(), AMOS::Sequence_t::getGCContent(), AMOS::Contig_t::getGCContent(), AMOS::Sequence_t::getLength(), AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), AMOS::Contig_t::getUngappedLength(), AMOS::Sequence_t::operator=(), AMOS::Sequence_t::Sequence_t(), AMOS::Sequence_t::setBase(), AMOS::Sequence_t::setSequence(), AMOS::Sequence_t::uncompress(), and AMOS::Sequence_t::writeMessage().

const NCode_t Read_t::NCODE = M_READ [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Sequence_t.

Definition at line 60 of file Read_AMOS.hh.

Referenced by AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildReadMate(), getNCode(), and writeMessage().

const ReadType_t AMOS::Read_t::NULL_READ = 0 [static]

Definition at line 62 of file Read_AMOS.hh.

Referenced by clear(), Read_t(), setType(), and writeMessage().

const ReadType_t AMOS::Read_t::OTHER = 'X' [static]

Definition at line 63 of file Read_AMOS.hh.

Referenced by setType().

const uint8_t AMOS::Sequence_t::QUAL_BITS = 0x3F [static, protected, inherited]

quality bit mask

Definition at line 52 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::uncompress().

uint8_t* AMOS::Sequence_t::qual_m [protected, inherited]

uncompressed qual data

Definition at line 42 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::clear(), AMOS::Sequence_t::compress(), AMOS::Sequence_t::getBase(), AMOS::Sequence_t::Sequence_t(), AMOS::Sequence_t::setBase(), AMOS::Sequence_t::setSequence(), and AMOS::Sequence_t::~Sequence_t().

const uint8_t AMOS::Sequence_t::SEQ_BITS = 0xC0 [static, protected, inherited]

sequence bit mask

Definition at line 51 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

uint8_t* AMOS::Sequence_t::seq_m [protected, inherited]

compressed seq and qual data or uncompressed seq

Definition at line 41 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::clear(), AMOS::Sequence_t::compress(), AMOS::Sequence_t::getBase(), AMOS::Contig_t::getGCContent(), AMOS::Sequence_t::Sequence_t(), AMOS::Sequence_t::setBase(), and AMOS::Sequence_t::~Sequence_t().

const uint8_t AMOS::Sequence_t::THYMINE_BITS = 0xC0 [static, protected, inherited]

'T' bit

Definition at line 50 of file Sequence_AMOS.hh.

Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

const ReadType_t AMOS::Read_t::TRANSPOSON = 'T' [static]

Definition at line 68 of file Read_AMOS.hh.

Referenced by setType().

const ReadType_t AMOS::Read_t::WALK = 'W' [static]

Definition at line 67 of file Read_AMOS.hh.

Referenced by setType().

AMOS::Read_t Class Reference

Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation


Public Member Functions
	Read_t ()
	Constructs an empty Read_t object.
	Read_t (const Read_t &source)
	Copy constructor.
	~Read_t ()
	Destroys a Read_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
const std::vector< int16_t > &	getBasePositions () const
	Get the base call positions.
std::vector< int16_t > &	getBasePositions ()
	Get the base call positions.
Range_t	getClearRange ()
	Get the generic clear range.
ID_t	getFragment () const
	Get the parent fragment IID.
Pos_t	getFragmentPosition ()
	Get the approximate position on the parent fragment.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
Range_t	getQualityClearRange ()
	Get the quality score clear range.
ReadType_t	getType () const
	Get the type of read.
Range_t	getVectorClearRange ()
	Get the vector sequence clear range.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setBasePositions (const std::vector< int16_t > &bcp)
	Set the base call positions.
void	setClearRange (Range_t clear)
	Set the generic clear range.
void	setFragment (ID_t frag)
	Set the parent fragment IID.
void	setFragmentPosition (Pos_t pos)
	Set the approximate position on the parent fragment.
void	setQualityClearRange (Range_t qclear)
	Set the quality score clear range.
void	setType (ReadType_t type)
	Set the type of read.
void	setVectorClearRange (Range_t vclear)
	Set the vector sequence clear range.
virtual void	writeMessage (Message_t &msg) const
	Writes data to a Message object.
void	compress ()
	Compress the internal representation of this sequence.
void	uncompress ()
	Uncompress the internal representation of this sequence.
std::pair< char, char >	getBase (Pos_t index) const
	Get a single base and its quality score.
virtual double	getGCContent (const Range_t &rng) const
	Get the gc content of the sequence.
virtual double	getGCContent () const
	Get the gc content of the sequence.
Size_t	getLength () const
	Get the length of the sequence.
std::string	getQualString () const
	Get the quality score string.
std::string	getQualString (Range_t range) const
	Get a quality score substring.
std::string	getSeqString () const
	Get the sequence base string.
std::string	getSeqString (Range_t range) const
	Get a sequence base substring.
bool	isCompressed () const
	Checks if the sequence data is compressed.
void	setBase (char seqchar, char qualchar, Pos_t index)
	Set a sequence base and its quality score.
void	setSequence (const char seq, const char qual)
	Set the entire sequence.
void	setSequence (const std::string &seq, const std::string &qual)
	Set the entire sequence.
const std::string &	getComment () const
	Get the comment string.
const Status_t	getStatus () const
	Get the status value.
void	setComment (const std::string &comment)
	Set the comment string.
void	setStatus (Status_t status)
	Set the status value.
const std::string &	getEID () const
	Get the external ID.
ID_t	getIID () const
	Get the internal ID.
bool	isRemoved () const
	Check if the object is waiting to be removed from the bank.
bool	isModified () const
	Check if the object has been modified.
bool	isFlagA () const
	Check the value of flag A.
bool	isFlagB () const
	Check the value of flag B.
void	setEID (const std::string &eid)
	Set the external ID.
void	setFlagA (bool flag)
	Set flag A.
void	setFlagB (bool flag)
	Set flag B.
void	setIID (ID_t iid)
	Set the internal ID.
Static Public Attributes
static const NCode_t	NCODE = M_READ
	The NCode type identifier for this object.
static const ReadType_t	NULL_READ = 0
static const ReadType_t	OTHER = 'X'
static const ReadType_t	END = 'E'
static const ReadType_t	CONTIG = 'C'
static const ReadType_t	BAC = 'B'
static const ReadType_t	WALK = 'W'
static const ReadType_t	TRANSPOSON = 'T'
Protected Member Functions
virtual void	readRecord (std::istream &fix, std::istream &var)
	Read selected class members from a biserial record.
virtual void	readRecordFix (std::istream &fix)
	Read selected class members from a fixed store only.
virtual void	writeRecord (std::ostream &fix, std::ostream &var) const
	Write selected class members to a biserial record.
Static Protected Member Functions
static uint8_t	compress (char seqchar, char qualchar)
	Compresses a sequence char and quality char into a single byte.
static std::pair< char, char >	uncompress (uint8_t byte)
	Uncompresses a byte into a sequence and quality char.
Protected Attributes
uint8_t *	seq_m
	compressed seq and qual data or uncompressed seq
uint8_t *	qual_m
	uncompressed qual data
Size_t	length_m
	length of the sequence and quality data
ID_t	iid_m
	internal ID (integer AMOS identifier)
std::string	eid_m
	external ID (anything you want sans newlines)
BankFlags_t	flags_m
	bank flags, derived classes may use "nibble"
Static Protected Attributes
static const uint8_t	COMPRESS_BIT = 0x1
	compressed sequence flag
static const uint8_t	ADENINE_BITS = 0x0
	'A' bit
static const uint8_t	CYTOSINE_BITS = 0x40
	'C' bit
static const uint8_t	GUANINE_BITS = 0x80
	'G' bit
static const uint8_t	THYMINE_BITS = 0xC0
	'T' bit
static const uint8_t	SEQ_BITS = 0xC0
	sequence bit mask
static const uint8_t	QUAL_BITS = 0x3F
	quality bit mask